C.H. MAK

In conjunction with experiments in Prof. Qin's group, we are trying to understand the precise nature of nucleic acid-ion interactions and how they influence peptide-RNA binding. Using large-scale computer simulations, we can study how counterions condense onto nucleic acids, how the diffuse counterions cloud renormalizes the backbone-backbone interactions to stabilize the tertiary structure of the nucleic acid, and how the peptide-RNA are mediated by electrostatics of the counterions. To effectively carry out these simulations involving large number of charges, we have developed efficient linear-scaling methods for computing the electrostatic interactions, which is the universal bottleneck in all large-scale computer simulations of highly charged systems... We continue to engage in the fundamental development of simulation algorithms that would enable chemists and molecular biologists to carry out calculations for large-scale and complex classical and quantum systems. Some of these..